asivache 63b709d992 When remapping the read, set MAPQ, CIGAR etc to 0/null for unmapped reads. This is not required according to spec but current samtools jdk otherwise dies in STRICT validation mode. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5089 348d0f76-0448-11de-a6fe-93d51630548a		2011-01-26 19:49:07 +00:00
..
config	Provide a default logger, some config settings, and some doc updates.	2009-04-29 02:06:05 +00:00
src	When remapping the read, set MAPQ, CIGAR etc to 0/null for unmapped reads. This is not required according to spec but current samtools jdk otherwise dies in STRICT validation mode.	2011-01-26 19:49:07 +00:00
test	added integration test for --sites_only option	2011-01-26 14:58:15 +00:00